The California sea lion (Zalophus californianus) has been a focal point for sensory, communication, cognition, and neurological disease studies in marine mammals. However, as a scientific community, we lack a noninvasive approach to investigate the anatomy and size of brain structures in this species and other free-ranging, live marine mammals. In this article, we provide the first anatomically labeled, magnetic resonance imaging-based atlas derived from a live marine mammal, the California sea lion. The brain of the California seal lion contained more secondary gyri and sulci than the brains of terrestrial carnivores. The olfactory bulb was present but small. The hippocampus of the California sea lion was found mostly in the ventral position with very little extension dorsally, quite unlike the canids and the mustelids, in which the hippocampus is present in the ventral position but extends dorsally above the thalamus. In contrast to the canids and the mustelids, the pineal gland of the California sea lion was strikingly large. In addition, we report three-dimensional reconstructions and volumes of cerebrospinal fluid, cerebral ventricles, total white matter (WM), total gray matter (GM), cerebral hemispheres (WM and GM), cerebellum and brainstem combined (WM and GM), and hippocampal structures all derived from magnetic resonance images. These measurements are the first to be determined for any pinniped species. In California sea lions, this approach can be used not only to relate cognitive and sensory capabilities to brain size but also to investigate the neurological effects of exposure to neurotoxins such as domoic acid.